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MB Sample ID: SA158969
| Local Sample ID: | NEG_APC_m830_8 |
| Subject ID: | SU001784 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001784 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| NEG_APC_m830_8 | SA158969 | FL018510 | APC | Genotype |
Collection:
| Collection ID: | CO001777 |
| Collection Summary: | Control (Lgr5–EGFP-IRES-CreERT2 Apc+/+) or experimental (Lgr5–EGFP-IRES-CreERT2 Apcfl/fl) adult mice were administered tamoxifen (80 mg/kg) daily via intraperitoneal injection for 4 consecutive days to induce Cre expression. Fourteen days following induction mice were sacrificed (cervical dislocation) and their intestinal cells were harvested for organoid culture of WT or Apc deficient intestinal stem cells. |
| Sample Type: | Intestine |
Treatment:
| Treatment ID: | TR001797 |
| Treatment Summary: | no treatment was applied |
Sample Preparation:
| Sampleprep ID: | SP001790 |
| Sampleprep Summary: | Following aqueous extraction using cold methanol and water (v:v, 1:1), 1 ml of pre-chilled dichloromethane (DCM)/methanol (v:v, 3:1) was added to the organoid samples. Samples were bead-beaten for 40 seconds followed by five minutes of chilling on dry ice. This procedure was repeated three times before being centrifuged for 10 mins at 21,000 rcf at 4ºC. A total of 600 μl of supernatant from each sample was transferred to a glass vial. Another 200 μl of supernatant from each sample was pooled into a 15-ml Falcon tube to form a quantity control (QC) sample and split into several aliquots of 600 μl each. An extraction blank sample was included to control for any potential contaminant introduced throughout the extraction process. Samples were dried by evaporation over night at room temperature and stored at -40˚C until further analysis. The dried extracts were reconstituted in 100 μl of water/acetonitrile (ACN)/isopropanol (IPA), (v:v:v, 1:1:3,). The lipids were dissolved by vigorous vortexing for five minutes, followed by five minutes of sonication. This step was repeated three times to allow the dry extracts to thoroughly dissolve in the solvent. Samples were subsequently centrifuged at 21,000 rcf for 10 minutes at 4ºC and transferred to 150-μl glass inserts placed in glass vials (Waters). |
Combined analysis:
| Analysis ID | AN002780 | AN002781 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Acquity UPLC | Acquity UPLC |
| Column | Waters Acquity C18 CSH (10 x 2.1mm,1.7um) | Waters Acquity C18 CSH (10 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Waters Synapt G2 S QTOF | Waters Synapt G2 S QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH002057 |
| Instrument Name: | Acquity UPLC |
| Column Name: | Waters Acquity C18 CSH (10 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002576 |
| Analysis ID: | AN002780 |
| Instrument Name: | Waters Synapt G2 S QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | refer to Methodology.docx |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | jli_20210217_034113_PR_MS_Methodology.docx |
| MS ID: | MS002577 |
| Analysis ID: | AN002781 |
| Instrument Name: | Waters Synapt G2 S QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | refer to Methodology.docx |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | jli_20210217_034113_PR_MS_Methodology.docx |
